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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GeomxTools
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* checking for file ‘GeomxTools/DESCRIPTION’ ... OK
* preparing ‘GeomxTools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd’ using rmarkdown
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: ggplot2
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
Attaching package: 'EnvStats'
The following objects are masked from 'package:stats':
predict, predict.lm
The following object is masked from 'package:base':
print.default
--- finished re-building ‘Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd’
--- re-building ‘GeomxSet_coercions.Rmd’ using rmarkdown
Attaching SeuratObject
Attaching sp
Calculating gene variances
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Calculating feature variances of standardized and clipped values
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Centering and scaling data matrix
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Warning in irlba(A = t(x = object), nv = npcs, ...) :
You're computing too large a percentage of total singular values, use a standard svd instead.
Computing nearest neighbor graph
Computing SNN
Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session
21:49:47 UMAP embedding parameters a = 0.9922 b = 1.112
21:49:47 Read 83 rows and found 30 numeric columns
21:49:47 Using Annoy for neighbor search, n_neighbors = 30
21:49:47 Building Annoy index with metric = cosine, n_trees = 50
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**************************************************|
21:49:47 Writing NN index file to temp file /tmp/Rtmpb2v71Z/file6f49cd66aac
21:49:47 Searching Annoy index using 1 thread, search_k = 3000
21:49:47 Annoy recall = 100%
21:49:48 Commencing smooth kNN distance calibration using 1 thread
21:49:49 Initializing from normalized Laplacian + noise
21:49:49 Commencing optimization for 500 epochs, with 1430 positive edges
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21:49:50 Optimization finished
Calculating gene variances
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix
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|======================================================================| 100%
Computing nearest neighbor graph
Computing SNN
21:49:52 UMAP embedding parameters a = 0.9922 b = 1.112
21:49:52 Read 199 rows and found 30 numeric columns
21:49:52 Using Annoy for neighbor search, n_neighbors = 30
21:49:52 Building Annoy index with metric = cosine, n_trees = 50
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
21:49:52 Writing NN index file to temp file /tmp/Rtmpb2v71Z/file6f49713165b3
21:49:52 Searching Annoy index using 1 thread, search_k = 3000
21:49:52 Annoy recall = 100%
21:49:53 Commencing smooth kNN distance calibration using 1 thread
21:49:54 Initializing from normalized Laplacian + noise
21:49:54 Commencing optimization for 500 epochs, with 7298 positive edges
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
21:49:55 Optimization finished
Quitting from lines 313-314 (GeomxSet_coercions.Rmd)
Error: processing vignette 'GeomxSet_coercions.Rmd' failed with diagnostics:
there is no package called 'SpatialExperiment'
--- failed re-building ‘GeomxSet_coercions.Rmd’
--- re-building ‘Protein_in_GeomxTools.Rmd’ using rmarkdown
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
--- finished re-building ‘Protein_in_GeomxTools.Rmd’
SUMMARY: processing the following file failed:
‘GeomxSet_coercions.Rmd’
Error: Vignette re-building failed.
Execution halted
